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SMTL ID : 8c8b.1

Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 48).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x U1L: 4-[[(2~{S})-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-~{N}-prop-2-enyl-quinazoline-2-carboxamide(Non-covalent)

U1L.1:

13 residues within 4Å:

Chain A: H.35, H.37, S.38, D.39, H.40, H.96, D.118, T.143, Y.182, S.183, H.297
Ligands: ZN.2, ZN.3

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:T.143, A:Y.182
Hydrogen bonds: A:D.39, A:H.297
Water bridges: A:S.38, A:S.183

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	6 residues within 4Å: Chain A: H.35, H.37, H.96, D.118 Ligands: U1L.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.35, A:H.37, A:H.96, A:D.118
ZN.3:	5 residues within 4Å: Chain A: D.39, H.40, D.118 Ligands: U1L.1, ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.39, A:H.40, A:D.118, H₂O.1, H₂O.6

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bielinski, M. et al., Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target. Chem Sci (2024)

Release Date

2024-01-31

Peptides

DNA cross-link repair 1A protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA cross-link repair 1A protein

Related Entries With Identical Sequence

5nzw.1 | 5nzx.1 | 5nzy.1 | 5q1j.1 | 5q1k.1 | 5q1l.1 | 5q1m.1 | 5q1n.1 | 5q1o.1 | 5q1p.1 | 5q1q.1 | 5q1r.1 | 5q1s.1 | 5q1t.1 | 5q1u.1 | 5q1v.1 | 5q1w.1 | 5q1x.1 | 5q1y.1 | 5q1z.1 | 5q20.1 | 5q22.1 | 5q23.1 | 5q24.1 | 5q25.1 | 5q26.1 | 5q27.1 | 5q28.1 | 5q29.1 | 5q2a.1 more...less...

5q2b.1 | 5q2c.1 | 5q2d.1 | 5q2e.1 | 5q2f.1 | 5q2g.1 | 5q2h.1 | 5q2i.1 | 5q2j.1 | 5q2k.1 | 5q2l.1 | 5q2m.1 | 5q2n.1 | 5q2o.1 | 5q2p.1 | 5q2q.1 | 5q2r.1 | 5q2s.1 | 5q2t.1 | 5q2u.1 | 5q2v.1 | 5q2w.1 | 5q2x.1 | 5q2y.1 | 5q2z.1 | 5q30.1 | 5q31.1 | 5q32.1 | 5q33.1 | 5q34.1 | 5q35.1 | 5q36.1 | 5q37.1 | 5q38.1 | 5q39.1 | 5q3a.1 | 5q3b.1 | 5q3c.1 | 5q3d.1 | 5q3e.1 | 5q3f.1 | 5q3g.1 | 5q3h.1 | 5q3i.1 | 5q3j.1 | 5q3k.1 | 5q3l.1 | 5q3m.1 | 5q3n.1 | 5q3o.1 | 5q3p.1 | 5q3q.1 | 5q3r.1 | 5q3s.1 | 5q3t.1 | 5q3u.1 | 5q3v.1 | 5q3w.1 | 5q3x.1 | 5q3y.1 | 5q3z.1 | 5q40.1 | 5q41.1 | 5q42.1 | 5q43.1 | 5q44.1 | 5q45.1 | 5q46.1 | 5q47.1 | 5q48.1 | 5q49.1 | 5q4a.1 | 5q4b.1 | 5q4c.1 | 5q4d.1 | 5q4e.1 | 5q4f.1 | 5q4g.1 | 5q4h.1 | 5q4i.1 | 5q4j.1 | 5q4k.1 | 5q4l.1 | 5q4m.1 | 5q4n.1 | 5q4o.1 | 5q4p.1 | 5q4q.1 | 5q4r.1 | 5q4s.1 | 5q4t.1 | 5q4u.1 | 5q4v.1 | 5q4w.1 | 5q4x.1 | 5q4y.1 | 5q4z.1 | 5q50.1 | 5q51.1 | 5q52.1 | 5q53.1 | 5q54.1 | 5q55.1 | 5q56.1 | 5q57.1 | 5q58.1 | 5q59.1 | 5q5a.1 | 5q5b.1 | 5q5c.1 | 5q5d.1 | 5q5e.1 | 5q5f.1 | 5q5g.1 | 5q5h.1 | 5q5i.1 | 5q5j.1 | 5q5k.1 | 5q5l.1 | 5q5m.1 | 5q5n.1 | 5q5o.1 | 5q5p.1 | 5q5q.1 | 5q5r.1 | 5q5s.1 | 5q5t.1 | 5q5u.1 | 5q5v.1 | 5q5w.1 | 5q5x.1 | 5q5y.1 | 5q5z.1 | 5q60.1 | 5q61.1 | 5q62.1 | 5q63.1 | 5q64.1 | 5q65.1 | 5q66.1 | 5q67.1 | 5q68.1 | 5q69.1 | 5q6a.1 | 5q6b.1 | 5q6c.1 | 5q6d.1 | 5q6e.1 | 5q6f.1 | 5q6g.1 | 5q6h.1 | 5q6i.1 | 5q6j.1 | 5q6k.1 | 5q6l.1 | 5q6m.1 | 5q6n.1 | 5q6o.1 | 5q6p.1 | 5q6q.1 | 5q6r.1 | 5q6s.1 | 5q6t.1 | 5q6u.1 | 5q6v.1 | 5q6w.1 | 5q6x.1 | 5q6y.1 | 5q6z.1 | 5q70.1 | 5q71.1 | 5q72.1 | 5q73.1 | 5q74.1 | 5q75.1 | 5q76.1 | 5q77.1 | 5q78.1 | 5q79.1 | 5q7a.1 | 5q7b.1 | 5q7c.1 | 5q7d.1 | 5q7e.1 | 5q7f.1 | 5q7g.1 | 5q7h.1 | 5q7i.1 | 5q7j.1 | 5q7k.1 | 5q7l.1 | 5q7m.1 | 5q7n.1 | 5q7o.1 | 5q7p.1 | 5q7q.1 | 5q7r.1 | 5q7s.1 | 5q7t.1 | 5q7u.1 | 5q7v.1 | 5q7w.1 | 5q7x.1 | 5q7y.1 | 5q7z.1 | 5q80.1 | 5q81.1 | 5q82.1 | 5q83.1 | 5q84.1 | 5q85.1 | 5q86.1 | 5q87.1 | 5q88.1 | 5q89.1 | 5q8a.1 | 5q8b.1 | 5q8c.1 | 5q8d.1 | 5q8e.1 | 5q8f.1 | 5q8g.1 | 5q8h.1 | 5q8i.1 | 5q8j.1 | 5q8k.1 | 5q8l.1 | 5q8m.1 | 5q8n.1 | 5q8o.1 | 5q8p.1 | 5q8q.1 | 5q8r.1 | 5q8s.1 | 5q8t.1 | 5q8u.1 | 5q8v.1 | 5q8w.1 | 5q8x.1 | 5q8y.1 | 5q8z.1 | 5q90.1 | 5q91.1 | 5q92.1 | 5q93.1 | 5q94.1 | 5q95.1 | 5q96.1 | 5q97.1 | 5q98.1 | 5q99.1 | 5q9a.1 | 5q9b.1 | 5q9c.1 | 5q9d.1 | 5q9e.1 | 5q9f.1 | 5q9g.1 | 5q9h.1 | 5q9i.1 | 5q9j.1 | 5q9k.1 | 5q9l.1 | 5q9m.1 | 5q9n.1 | 5q9o.1 | 5q9p.1 | 5q9q.1 | 5q9r.1 | 5q9s.1 | 5q9t.1 | 5q9u.1 | 5q9v.1 | 5q9w.1 | 5q9x.1 | 5q9y.1 | 5q9z.1 | 5qa0.1 | 5qa1.1 | 5qa2.1 | 8c8d.1 | 8c8s.1

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